Allele API Help Page
The IPD-IMGT/HLA Database has developed a REST API to allow users to make their own queries to the database.
The entry point for the IPD API is:
| Type | Value |
|---|---|
| Entry Point: | https://www.ebi.ac.uk/cgi-bin/ipd/api/allele? |
The API uses a query language that allows to concatenate search parameters with various operators. The query string is then parsed to build a mongodb query dictionary. Coverage of the mongo query interface isn't 100% implemented yet. Here's what's available:
| operator | example |
|---|---|
| $eq | eq(name,"West and Sons") |
| $gte | gte(id,6) |
| $gt | gt(id,6) |
| $lte | lte(id,3) |
| $lt | lt(id,3) |
| $ne | ne(closed,true) |
| $size | size(grades,4) |
| $in | in(restaurant_id,["8165423","5827429"]) |
| $nin | nin(id,[1,2,3,4,5]) |
| $all | all(address.coord,["-47.9327","-82.6261"]) |
| $and | and(eq(grades.score,5),eq(borough,"Buckinghamshire")) |
| $or | or(eq(id,1),eq(borough,"Buckinghamshire")) |
| $not | not(size(grades,0)) |
Example; only return cells who have the sex attribute equal to 'M' or 'F' and ethnics equal to 'American'
GET /cell?query=and(eq(ethnics,American),or(eq(sex, M), eq(sex, F)))There are also extra operators that wrap $regex providing a more predictable query without the full power or danger associated with PCREs.
| operator | example |
|---|---|
| startsWith | startsWith(name, "We") |
| endsWith | endsWith(address.street, "Road") |
| contains | contains(borough, "shire") |
Data types
In addition to the string, number, boolean and null types, the parser supports Date parsing.
| type | format | example usage |
|---|---|---|
| date | yyyy-mm-dd,yyyy/mm/dd,yyyy-mm, yyyy/mm, yyyy | gt(date_modified,date("2015-04-28")) |
The API can be accessed from the following points:
| Name | URL | Description | Parameters |
|---|---|---|---|
| index | / | API index page | - |
| allele list | /allele | Allele list page | project, limit, query, next, prev, fields, sort |
| allele download | /allele/download | Download a list of allele sequences of type type, where type can be 'protein', 'genomic' or 'coding' | project, query, type |
| single allele | /allele/<accession> | Single allele data | project |
| cell list | /cell | Cell list page | limit, query, next, prev, fields, sort |
| single cell | /cell/<cellid> | - |
{
"accession": "HLA00001",
"cell_entries": [
{
"cell_name": "COX",
"cellid": "10429",
"ethnic_origin": "Caucasoid - South Africa, Southern Africa"
},
{
"cell_name": "MOLT-4",
"cellid": "11094",
"ethnic_origin": "Unknown"
},
{
"cell_name": "7550800303",
"cellid": "17414",
"ethnic_origin": "Oriental - China, Asia"
},
{
"cell_name": "LCL721",
"cellid": "10972",
"ethnic_origin": "Unknown"
},
{
"cell_name": "APD",
"cellid": "10258",
"ethnic_origin": "Caucasoid - Netherlands, Europe"
},
{
"cell_name": "B4702",
"cellid": "16068",
"ethnic_origin": "Oriental - Chinese, China, Asia"
},
{
"cell_name": "PP",
"cellid": "11275",
"ethnic_origin": "Caucasoid - England, Europe"
}
],
"citations": [
{
"authors": "Girdlestone J, Girdlestone J",
"journal": "Nucleic Acids Res",
"pubmed": "2251137",
"title": "Nucleotide sequence of an HLA-A1 gene",
"volume": "18:6701-6701",
"year": "1990"
},
{
"authors": "Parham P, Lomen CE, Lawlor DA, Ways JP, Holmes N, Coppin HL, Salter RD, Wan AM, Ennis PD",
"journal": "Proc Natl Acad Sci U S A",
"pubmed": "3375250",
"title": "Nature of polymorphism in HLA-A, -B, and -C molecules",
"volume": "85:4005-9",
"year": "1988"
},
{
"authors": "Stewart CA, Horton R, Allcock RJ, Ashurst JL, Atrazhev AM, Coggill P, Dunham I, Forbes S, Halls K, Howson JM, Humphray SJ, Hunt S, Mungall AJ, Osoegawa K, Palmer S, Roberts AN, Rogers J, Sims S, Wang Y, Wilming LG, Elliott JF, de Jong PJ, Sawcer S, Todd JA, Trowsdale J, Beck S",
"journal": "Genome Res",
"pubmed": "15140828",
"title": "Complete MHC haplotype sequencing for common disease gene mapping",
"volume": "14:1176-87",
"year": "2004"
},
{
"authors": "Zhu F, He Y, Zhang W, He J, He J, Xu X, Yan L",
"journal": "Int J Immunogenet",
"pubmed": "19735485",
"title": "Analysis of the complete genomic sequence of HLA-A alleles in the Chinese Han population.",
"volume": "36:351-360",
"year": "2009"
},
{
"authors": "Horton R, Gibson R, Coggill P, Miretti M, Allcok RJ, Almeida J, Forbes S, Gilbert JGR, Halls K, Harrow JL, Hart E, Howe K, Jackson DK, Palmer S, Roberts AN, Sims S, Stewart CA, Traherne JA, Trevanion S, Wilming L, Rogers J, de Jong PJ, Elliott JF, Sawcer S, Todd JA, Trowsdale J, Beck S",
"journal": "Immunogenetics",
"pubmed": "18193213",
"title": "Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project",
"volume": "60:1-18",
"year": "2008"
},
{
"authors": "Laforet M, Laforet M, Froelich N, Froelich N, Parissiadis A, Parissiadis A, Pfeiffer B, Pfeiffer B, Schell A, Schell A, Faller B, Faller B, Woehl-Jaegle ML, Woehl-Jaegle ML, Cazenave JP, Cazenave JP, Tongio MM, Tongio MM",
"journal": "Tissue Antigens",
"pubmed": "9349617",
"title": "A nucleotide insertion in exon 4 is responsible for the absence of expression of an HLA-A*01 allele",
"volume": "50:347-50",
"year": "1997"
},
{
"authors": "Lu L, Xu YP",
"journal": "Tissue Antigens",
"pubmed": "24673518",
"title": "Genomic full-length sequence of two HLA-A alleles, A*01:01:01:01 and A*01:03, identified by cloning and sequencing.",
"volume": "83:423-424",
"year": "2014"
}
],
"confirmation_status": {
"cells": 7,
"confirmed": true,
"laboratories": 8
},
"cwd": {
"version_2": "C",
"version_3": {
"AFA": "C",
"API": "C",
"EURO": "C",
"HIS": "C",
"MENA": "C",
"NAM": "C",
"Total": "C",
"UNK": "C"
}
},
"date_assigned": "01-AUG-89",
"date_deleted": null,
"date_modified": "16-DEC-98",
"date_released": "2021-04-20",
"dictionary": {
"data": {
"comments": null,
"expert_assigned": "A1",
"neural_assigned": "The allele was used for training of the Neural Network - A1",
"who_assigned": "A1"
},
"source": [
{
"cells_tested": "113",
"tested_by": "13 IHWC",
"type_assigned": "A1",
"year_tested": "2002"
},
{
"cells_tested": "34",
"tested_by": "International Cell Exchange UCLA",
"type_assigned": "A1 [98-100]",
"year_tested": "2008"
},
{
"cells_tested": "5612",
"tested_by": "NMDP",
"type_assigned": "A1 [99]",
"year_tested": "2008"
}
]
},
"feature": {
"coding": [
{
"length": 73,
"number": "1",
"start": 1,
"type": "exon"
},
{
"length": 270,
"number": "2",
"start": 74,
"type": "exon"
},
{
"length": 276,
"number": "3",
"start": 344,
"type": "exon"
},
{
"length": 276,
"number": "4",
"start": 620,
"type": "exon"
},
{
"length": 117,
"number": "5",
"start": 896,
"type": "exon"
},
{
"length": 33,
"number": "6",
"start": 1013,
"type": "exon"
},
{
"length": 48,
"number": "7",
"start": 1046,
"type": "exon"
},
{
"length": -4,
"number": "8",
"start": 1094,
"type": "exon"
}
],
"genomic": [
{
"length": 300,
"start": 1,
"type": "5utr"
},
{
"length": 73,
"number": "1",
"start": 301,
"type": "exon"
},
{
"length": 130,
"number": "1",
"start": 374,
"type": "intron"
},
{
"length": 270,
number": "2",
"start": 504,
"type": "exon"
},
{
"length": 241,
"number": "2",
"start": 774,
"type": "intron"
},
{
"length": 276,
"number": "3",
"start": 1015,
"type": "exon"
},
{
"length": 579,
"number": "3",
"start": 1291,
"type": "intron"
},
{
"length": 276,
"number": "4",
"start": 1870,
"type": "exon"
},
{
"length": 102,
"number": "4",
"start": 2146,
"type": "intron"
},
{
"length": 117,
"number": "5",
"start": 2248,
"type": "exon"
},
{
"length": 442,
"number": "5",
"start": 2365,
"type": "intron"
},
{
"length": 33,
"number": "6",
"start": 2807,
"type": "exon"
},
{
"length": 142,
"number": "6",
"start": 2840,
"type": "intron"
},
{
"length": 48,
"number": "7",
"start": 2982,
"type": "exon"
},
{
"length": 169,
"number": "7",
"start": 3030,
"type": "intron"
},
{
"length": 5,
"number": "8",
"start": 3199,
"type": "exon"
},
{
"length": -299,
"start": 3204,
"type": "3utr"
}
],
"protein": [
{
"length": 24,
"start": 1,
"type": "signal"
},
{
"length": 317,
"start": 25,
"type": "mature"
}
]
},
"insdc": [
"X55710",
"AL645935",
"Z93949",
"M24043",
"GU812295",
"AJ278305",
"HG794373",
"CR759913",
"EU445470"
],
"locus": "A*",
"name": "A*01:01:01:01",
"oid": "2.16.840.1.113883.13.252.1.1.1",
"omim": "142800",
"previous_nomenclature": "A*01010101",
"project": "HLA",
"reason_for_deletion": null,
"release_version": "3.44.0",
"secondary_names": "A*01011, A*0101, A1",
"sequence": {
"coding": "ATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAAGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATATGAAGGCCCACTCACAGACTGACCGAGCGAACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGACGGTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGATCACCAAGCGCAAGTGGGAGGCGGTCCATGCGGCGGAGCAGCGGAGAGTCTACCTGGAGGGCCGGTGCGTGGACGGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGCCCCTCACCCTGAGATGGGAGCTGTCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAGATAGAAAAGGAGGGAGTTACACTCAGGCTGCAAGCAGTGACAGTGCCCAGGGCTCTGATGTGTCTCTCACAGCTTGTAAAGTGTGA",
"genomic": "CAGGAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAGGGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTACGTAGGGTCCTTCATCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGTCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGAGGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAAGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATATGAAGGCCCACTCACAGACTGACCGAGCGAACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGACGGTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACTCCGAGACCCTTGTCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCGGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGTCGGGGCCAGGTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGCCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGATCACCAAGCGCAAGTGGGAGGCGGTCCATGCGGCGGAGCAGCGGAGAGTCTACCTGGAGGGCCGGTGCGTGGACGGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGGGTACCAGGGGCCACGGGGCGCCTCCCTGATCGCCTATAGATCTCCCGGGCTGGCCTCCCACAAGGAGGGGAGACAATTGGGACCAACACTAGAATATCACCCTCCCTCTGGTCCTGAGGGAGAGGAATCCTCCTGGGTTTCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCTGCTCTCTGACACAATTAAGGGATAAAATCTCTGAAGGAGTGACGGGAAGACGATCCCTCGAATACTGATGAGTGGTTCCCTTTGACACCGGCAGCAGCCTTGGGCCCGTGACTTTTCCTCTCAGGCCTTGTTCTCTGCTTCACACTCAATGTGTGTGGGGGTCTGAGTCCAGCACTTCTGAGTCTCTCAGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCCTTCTCAGGGAATAGAAGATTATCCCAGGTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGTGTCCTGTCCATTCTCAAGATGGCCACATGCGTGCTGGTGGAGTGTCCCATGACAGATGCAAAATGCCTGAATTTTCTGACTCTTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGCCCCTCACCCTGAGATGGGGTAAGGAGGGAGATGGGGGTGTCATGTCTCTTAGGGAAAGCAGGAGCCTCTCTGGAGACCTTTAGCAGGGTCAGGGCCCCTCACCTTCCCCTCTTTTCCCAGAGCTGTCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCTGAGATTTCTTGTCTCACTGAGGGTTCCAAGCCCCAGCTAGAAATGTGCCCTGTCTCATTACTGGGAAGCACCTTCCACAATCATGGGCCGACCCAGCCTGGGCCCTGTGTGCCAGCACTTACTCTTTTGTAAAGCACCTGTTAAAATGAAGGACAGATTTATCACCTTGATTACGGCGGTGATGGGACCTGATCCCAGCAGTCACAAGTCACAGGGGAAGGTCCCTGAGGACAGACCTCAGGAGGGCTATTGGTCCAGGACCCACACCTGCTTTCTTCATGTTTCCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTTAAGGCCCTGGCTCCTTTCTGGTATCTCACAGGACATTTTCTTCCCACAGATAGAAAAGGAGGGAGTTACACTCAGGCTGCAAGTAAGTATGAAGGAGGCTGATGCCTGAGGTCCTTGGGATATTGTGTTTGGGAGCCCATGGGGGAGCTCACCCACCCCACAATTCCTCCTCTAGCCACATCTTCTGTGGGATCTGACCAGGTTCTGTTTTTGTTCTACCCCAGGCAGTGACAGTGCCCAGGGCTCTGATGTGTCTCTCACAGCTTGTAAAGGTGAGAGCTTGGAGGGCCTGATGTGTGTTGGGTGTTGGGTGGAACAGTGGACACAGCTGTGCTATGGGGTTTCTTTGCGTTGGATGTATTGAGCATGCGATGGGCTGTTTAAGGTGTGACCCCTCACTGTGATGGATATGAATTTGTTCATGAATATTTTTTTCTATAGTGTGAGACAGCTGCCTTGTGTGGGACTGAGAGGCAAGAGTTGTTCCTGCCCTTCCCTTTGTGACTTGAAGAACCCTGACTTTGTTTCTGCAAAGGCACCTGCATGTGTCTGTGTTCGTGTAGGCATAATGTGAGGAGGTGGGGAGAGCACCCCACCCCCATGTCCACCATGACCCTCTTCCCACGCTGACCTGTGCTCCCTCTCCAATCATCTTTCCTGTTCCAGAGAGGTGGGGCTGAGGTGTCTCCATCTCTGTCTCAACTTCATGGTGCACTGAGCTGTAACTTCTTCCTTCCCTATTAAAA",
"protein": "MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSLTACKV"
},
"sequence_status": {
"end": 1098,
"full": true,
"start": 1,
"type": "gDNA"
},
"status": "PUBLIC"
}